Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “allele frequency changes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed2002

The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers.

We used the amplified fragment length polymorphism (AFLP) method to obtain genetic markers distinguishing two subspecies of willow warblers Phylloscopus trochilus that have different migratory behaviours but are not differentiated in mitochondrial DNA or at several microsatellite loci. With the inverse-polymerase chain reaction (PCR) approach we converted a dominant AFLP-marker to a codominant single nucleotide polymorphism (SNP). Across Scandinavia we typed 621 birds at the SNP locus AFLP-WW1 and we found a sigmoid change in allele frequencies centred around 62 degrees latitude. North of the latitudinal cline was a west-east cline. Both clines are narrower than one would expect from dispersal distances in willow warblers, which suggests that these are maintained by selection. The latitudinal cline at the locus AFLP-WW1 is paralleled by changes in several other traits, all of which might be maintained by a single selective force. The most plausible selection factor that we have identified is selection against hybrids because of inferior migratory behaviour. The selective force maintaining the east-west cline is less obvious. We discuss alternatives to the selection scenario, involving colonization history and asymmetric gene flow.

Animal Migration↗
PubMed2002

Extensive population subdivision of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) around the Iberian Peninsula indicated by microsatellite DNA variation.

The Atlantic Ocean-Mediterranean Sea junction has been proposed as an important phylogeographical area on the basis of concordance in genetic patterns observed at allozyme, mtDNA and microsatellite DNA markers in several marine species. This study presents microsatellite DNA data for a mobile invertebrate species in this area, the cuttlefish Sepia officinalis, allowing comparison of this relatively new class of DNA marker with previous allozyme results, and examination of the relative effects on gene flow of the Strait of Gibraltar and the Almería-Oran oceanographic front. Genetic variation at seven microsatellite loci screened in six samples from NE Atlantic and Mediterranean coasts of the Iberian Peninsula was high (mean Na = 9.6, mean H(e) = 0.725). Microsatellites detected highly significant subpopulation structuring (F(ST)= 0.061; R(ST) = 0.104), consistent with an isolation-by-distance model of low levels of gene flow. Distinct and significant clinal changes in allele frequencies between Atlantic and Mediterranean samples found at five out of seven loci, however indicate these results might be also consistent with an alternative model of secondary contact and introgression between previously isolated and divergent populations, as previously proposed for other marine species from the Atlantic-Mediterranean area. A pronounced 'step' change between SW Mediterranean samples associated with the Almería-Oran front suggests this oceanographic feature may represent a contemporary barrier to gene flow.

Animals↗
PubMed2001

Candidate gene analysis for loci affecting litter size and ovulation rate in swine.

A candidate gene approach was used to determine whether specific loci explain responses in ovulation rate (OR) and number of fully formed (FF), live (NBA), stillborn, and mummified pigs at birth observed in two lines selected for ovulation rate and litter size compared with a randomly selected control line. Line IOL was selected for an index of OR and embryonic survival for eight generations, followed by eight generations of two-stage selection for OR and litter size. Line C was selected at random for 16 generations. Line COL, derived from line C at Generation 8, underwent eight generations of two-stage selection. Lines IOL and C differed in mean EBV by 6.1 ova and 4.7 FF, whereas lines COL and C differed by 2.2 ova and 2.9 FF. Pigs of Generation 7 of two-stage selection lines were genotyped for the retinol binding protein 4 (RBP4, n = 190) and epidermal growth factor (EGF, n = 189) loci, whereas pigs of Generations 7 and 8 were genotyped for the estrogen receptor (ESR, n = 523), prolactin receptor (PRLR, n = 524), follicle-stimulating hormone beta (FSHbeta, n = 520), and prostaglandin-endoperoxide synthase 2 (PTGS2, n = 523) loci. Based on chi-square analysis for homogeneity of genotypic frequencies, distributions for PRLR, FSHbeta, and PTGS2 were different among lines (P < 0.005). Differences in gene frequencies between IOL vs C and COL vs C were 0.33 +/- 0.25 and 0.16 +/- 0.26 for PRLR, 0.35 +/- 0.20 and 0.15 +/- 0.24 for FSHbeta, and 0.16 +/- 0.16 and 0.08 +/- 0.18 for PTGS2. Although these differences are consistent with a model of selection acting on these loci, estimates of additive and dominance effects at these loci did not differ from zero (P > 0.05), and several of them had signs inconsistent with the changes in allele frequencies. We were not able to find significant associations between the polymorphic markers and phenotypes studied; however, we cannot rule out that other genetic variation within these candidate genes has an effect on the traits studied.

Animals↗
PubMed2003

Genetic structure along a gaseous organic pollution gradient: a case study with Poa annua L.

The population genetic composition of Poa annua L. was studied by starch electrophoresis along a transect running NE from an organic reagents factory at Shanghai, China. Five enzyme systems were stained. We have reached the following preliminary conclusions: (1). Organic pollution has dramatically changed genotypic frequencies at some loci of Poa annua populations. At polluted sites, significant deviations from Hardy-Weinberg equilibrium were observed on loci Sod-1 and Me due to the excess of heterozygote. Especially in the two nearest sites to pollution source, all the individuals were heterozygous at locus Sod-1. The data suggests that heterozygotes were more tolerant to organic pollution than homozygotes, indicating the fitness superiority of heterozygotes. (2). A tendency towards clinal changes of allele frequencies was found at some polymorphic loci. Frequencies of the common alleles at loci Sod-1, Me and Fe-1 increased as the distance to the pollution source increased. (3). The effective number of alleles per locus, and the observed and expected heterozygosity were much higher in the pollution series than in the clear control site (Botanic Park population), but genetic multiplicity (number of alleles per locus) was lower than for the control. (4). Most genetic variability was found within populations, and only 2.56% were among populations of the polluted series. However, 9.48% of the total genetic variation occurred among populations when including the Botanic Park population. The genetic identity between populations of the pollution series (0.9869-1.0000, mean 0.9941) was higher than those between the pollution series and the Botanic Park population. UPGMA divided the five populations into two groups. One contained the four polluted populations, and the other only contained the Botanic Park population.

Air Pollutants↗
PubMed1991

Relationship between allozymes, heterozygosity and morphological characters in red deer (Cervus elaphus), and the influence of selective hunting on allele frequency distribution.

Morphological characters in red deer (Cervus elaphus), which serve as criteria for selective hunting, were examined in relation to electrophoretic variation in three populations from the Vosges in eastern France. From the polymorphic loci examined, certain alleles at Idh-2, Me-1 and Acp-1 showed significant associations with a special development of body and antler characters selected for by hunters. Idh-2(125) was associated with larger hind foot length in females and a higher number of antler points in males. Me-1(90) and Acp-1(100) were associated with small spikes. The populations studied differed from one another in the duration and intensity of selective hunting and the increase or decrease in the respective allele frequencies could be explained by selection for large body size, a high number of antler points and against small spikes in yearlings, rather than by genetic drift. Among other morphological characters examined, the length of the main beam was significantly associated with the allele Acp-2(100). In contrast, no associations could be detected between overall heterozygosity and the development or the degree of asymmetry (in paired structures) of any of the morphological traits in question. Although no obvious differences in the overall values of polymorphism or heterozygosity were found between the populations, selective hunting leads towards a change in allele frequencies and eventually to the loss of one or the other rare allele.

Alleles↗
PubMed2003

Fixation probability and time in subdivided populations.

New alleles arising in a population by mutation ultimately are either fixed or lost. Either is possible, for both beneficial and deleterious alleles, because of stochastic changes in allele frequency due to genetic drift. Spatially structured populations differ from unstructured populations in the probability of fixation and the time that this fixation takes. Previous results have generally made many assumptions: that all demes contribute to the next generation in exact proportion to their current sizes, that new mutations are beneficial, and that new alleles have additive effects. In this article these assumptions are relaxed, allowing for an arbitrary distribution among demes of reproductive success, both beneficial and deleterious effects, and arbitrary dominance. The effects of population structure can be expressed with two summary statistics: the effective population size and a variant of Wright's F(ST). In general, the probability of fixation is strongly affected by population structure, as is the expected time to fixation or loss. Population structure changes the effective size of the species, often strongly downward; smaller effective size increases the probability of fixing deleterious alleles and decreases the probability of fixing beneficial alleles. On the other hand, population structure causes an increase in the homozygosity of alleles, which increases the probability of fixing beneficial alleles but somewhat decreases the probability of fixing deleterious alleles. The probability of fixing new beneficial alleles can be simply described by 2hs(1 - F(ST))N(e)/N(tot), where hs is the change in fitness of heterozygotes relative to the ancestral homozygote, F(ST) is a weighted version of Wright's measure of population subdivision, and N(e) and N(tot) are the effective and census sizes, respectively. These results are verified by simulation for a broad range of population structures, including the island model, the stepping-stone model, and a model with extinction and recolonization.

Alleles↗
PubMed1996

Genetic variation in Sri Lanka.

A population genetic study was designed to analyze genetic composition and population structure of the five main population groups (Sinhalese, Tamils, Moors, Burghers, and Malays) of Sri Lanka. Twentyseven polymorphic and three monomorphic loci were examined in all five populations. Several genetic markers, including subtype variation of HP, TF, PI, GC, ORM, and PGM1, were analyzed for the first time and helped to clarify the range of genetic variation for Sri Lankan populations. Many genetic systems (Rh, JK, ACP, ESD, HP, C3, TF, and GC) showed a high level of variation among the populations of Sri Lanka. However, at the individual level the Burgher population (a hybrid group between the Dutch and Portuguese and the local Sinhalese) showed European features, but its gene frequencies were either intermediate to its parental populations or more similar to the local Sinhalese. In the F statistic analysis all populations showed positive FIS values, ranging from 0.0305 in the Burghers to 0.1084 in the Malays; however, for a large number of loci the FIS values for the Burghers were negative, indicating the possible hybrid nature of this population. In genetic affinity studies the Burghers, Moors, and Malays showed a greater degree of isolation, but compared with the possible populations of their origin, the five populations of Sri Lanka tended to show some degree of affinity to each other. Our analysis therefore suggests that there is little evidence of disruptive selection; however, restricted gene flow favors the change of allele frequency toward the local Sinhalese and Tamil populations.

Ethnicity↗
PubMed1983

Mice selected for age of puberty: reverse selection and reproductive characteristics.

Previous investigations have hypothesized a link between regulation of population size in various rodent species and changes in allele frequencies for certain loci that exert their effects on particular behaviors or processes related to reproduction. Drickamer (1981a) has shown that age of first vaginal estrus can be shifted by artificial selection and that there is a relatively high heritability for this trait in laboratory Mus. This paper reports on two related experiments, one a test of reverse selection on strains of mice previously selected for early and late first vaginal estrus, and the other a compilation of data for a variety of traits related to reproduction for the original base stock and four artificially selected stocks. The original selection for early and late onset of puberty did not result in fixation of the trait-enough residual variation remained so that in eight generations of selection it was possible to significantly reverse the timing of first estrus. Traits related to reproduction including litter size, pup weight, survival of pups to 21 days, weight at 21 days, fertility and birth intervals all were not affected by the selection process across all five stocks tested. These results are discussed with regard to changes in puberty and generation time in Mus as a factor in population regulation.

Animals↗
PubMed2004

[Analysis of the DRD4 gene polymorphism in populations of Russia and neighboring countries].

Allele and genotype frequencies of the VNTR polymorphism in the third exon of human DRD4 gene were determined in 544 individuals living in Russia (Russians, Bashkirs, Tatars, and Mordovians) and in the neighboring countries (Kazakhs and Ukrainians). The data obtained were compared with the allele frequency distribution patterns reported for the populations of Eurasia. Similarly to other Eurasian populations, in our population samples R4 allele was prevalent (64 to 87%). The frequency of this allele in the populations of Western Europe constitute 61 to 71%, while in the populations of Asia it varies from 74 to 96%. In this respect, the populations studied occupied the intermediate position. In the samples examined the R7 allele frequency decreased from 7% in Ukrainians to 1% in Bashkirs, while in Kazakhs and Mordovians the allele was absent. This finding was consistent with the R7 allele distribution pattern in the populations of Eurasia, characterized by higher frequency in the West and lower frequency or absence of the allele in the East. In the group of 22 Eurasian populations, the R7 allele frequency negatively correlated with the frequency of the R4 allele (r = -0.86 at P < 0.001). Unlike the R4 and R7 alleles, the frequency of which changed in the eastward direction, the R2 allele frequency distribution displayed slightly expressed latitudinal increase southwards. The DRD4 genotype distribution deviated from the equilibrium in most of the samples examined. In some samples, statistically significant increase of the R2/R2 homozygotes frequency was demonstrated. One of the possible explanations of this phenomenon is assortative mating with respect to phenotypic (behavioral) allele manifestation. The data obtained can serve as the basis for the investigation of the possible role of the DRD4 alleles as the risk factors for the development of alcoholism and other types of addictions.

Alleles↗
PubMed2000

Quantitative genetic models for the balance between migration and stabilizing selection.

The evolution of a quantitative trait subject to stabilizing selection and immigration, with the immigrants deviating from the local optimum, is considered under a number of different models of the underlying genetic basis of the trait. By comparing exact predictions under the infinitesimal model obtained using numerical methods with predictions of a simplified approximate model based on ignoring linkage disequilibrium, the increase in the expressed genetic variance as a result of linkage disequilibrium generated by migration is shown to be relatively small and negligible, provided that the genetic variance relative to the squared deviation of immigrants from the local optimum is sufficiently large or selection and migration is sufficiently weak. Deviation from normality is shown to be less important by comparing predictions of the infinitesimal model with a model presupposing normality. For a more realistic symmetric model, involving a finite number of loci only, no linkage and equal effects and frequencies across loci, additional changes in the genetic variance arise as a result of changes in underlying allele frequencies. Again, provided that the genetic variance relative to the squared deviation of the immigrants from the local optimum is small, the difference between the predictions of infinitesimal and the symmetric model are small unless the number of loci is very small. However, if the genetic variance relative to the squared deviation of the immigrants from the local optimum is large, or if selection and migration are strong, both linkage disequilibrium and changes in the genetic variance as a result of changes in underlying allele frequencies become important.

Base Sequence↗
PubMed1988

An experimental analysis of the relationships between fitness components and malic enzyme genotypes in Tribolium confusum.

The hypothesis that natural selection is capable of maintaining allozyme variation in natural populations was tested using a species of flour beetles, Tribolium confusum. We selected a polymorphic locus (a locus encoding variation for malic enzyme) in an experimental population of T. confusum and scored the genotypes at this locus for a series of fitness components on different flour types. Measurements included survival rate, development time, fecundity, and rate of egg cannibalism. Flour type had significant effects on most traits. Significant differences among genotypes for fecundity and rates of egg cannibalism and the presence of genotype x flour type interactions for development time were demonstrated. Thus, changes in allele frequencies at the malic enzyme locus could in part be under the influence of natural selection. The existence of genotype x flour type interactions suggests that environmental heterogeneity could maintain allozyme variation at the malic enzyme locus.

Animals↗
PubMed2005

Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years.

It has been claimed that the system that delivers the products of plant breeding reduces the diversity of cultivated varieties leading to an increased genetic vulnerability. The main goal of our study was to monitor the temporal trends in genetic diversity over the past five decades among maize cultivars with the largest acreage in Central Europe. Our objectives were to (1) investigate how much of the genetic diversity present in important adapted open-pollinated varieties (OPVs) has been captured in the elite flint germ plasm pool, (2) examine changes in the genetic diversity among the most important commercial hybrids as well as in their dent and flint parents, (3) analyze temporal changes in allele frequencies between the dent and flint parental inbreds, and (4) investigate linkage disequilibrium (LD) trends between pairs of loci within the set of parental dent and flint lines. We examined 30 individuals of five prominent OPVs from Central Europe, 85 maize hybrids of economic importance, and their dent and flint parental components with 55 SSRs. LD was significant at probability level P=0.01 for 20.2% of the SSR marker pairs in the 82 dent lines and for 17.2% in the 66 flint lines. The dent and flint heterotic groups were clearly separated already at the beginning of hybrid breeding in Central Europe. Furthermore, the genetic variation within and among varieties decreased significantly during the five decades. The five OPVs contain numerous unique alleles that were absent in the elite flint pool. Consequently, OPVs could present useful sources for broadening the genetic base of elite maize breeding germ plasm.

Europe↗
PubMed2004

MHC polymorphism under host-pathogen coevolution.

The genes encoding major histocompatibility (MHC) molecules are among the most polymorphic genes known for vertebrates. Since MHC molecules play an important role in the induction of immune responses, the evolution of MHC polymorphism is often explained in terms of increased protection of hosts against pathogens. Two selective pressures that are thought to be involved are (1) selection favoring MHC heterozygous hosts, and (2) selection for rare MHC alleles by host-pathogen coevolution. We have developed a computer simulation of coevolving hosts and pathogens to study the relative impact of these two mechanisms on the evolution of MHC polymorphism. We found that heterozygote advantage per se is insufficient to explain the high degree of polymorphism at the MHC, even in very large host populations. Host-pathogen coevolution, on the other hand, can easily account for realistic polymorphisms of more than 50 alleles per MHC locus. Since evolving pathogens mainly evade presentation by the most common MHC alleles in the host population, they provide a selective pressure for a large variety of rare MHC alleles. Provided that the host population is sufficiently large, a large set of MHC alleles can persist over many host generations under host-pathogen coevolution, despite the fact that allele frequencies continuously change.

Computer Simulation↗
PubMedDate not supplied

Sensitivity of inbred and selectively bred mice to ethanol.

The Long-Sleep (LS) and Short-Sleep (SS) mice were bred for differences in sensitivity to ethanol as measured by duration of loss of the righting response (sleep time). The foundation population was a heterogeneous stock (HS) which was derived from a cross of eight inbred strains. Ethanol-induced sleep time and waking blood and brain ethanol levels were measured in the eight inbred strains, LS, SS and HS mice. The C3H and ISBI strains were quite resistant to ethanol as measured by sleep time, and only one, RIII, was very sensitive. Waking ethanol concentrations were similar for all of the inbreds, implying a narrow range of central nervous system sensitivity to ethanol. The HS mice had relatively short sleep times and blood ethanol levels equal to most of the inbred. The LS mice were significantly more, and the SS mice significantly less sensitive to ethanol than any of the inbreds or HS mice. These studies suggest that the extremes of CNS sensitivities to ethanol manifested by the LS and SS mice cannot be traced to any of the inbred strains, and must have arisen through the selection process by changes in allelic frequencies of those genes conferring ethanol sensitivity and resistance.

Animals↗
PubMed1997

Serotonin2A receptor gene polymorphism in mood disorders.

Genes that regulate the serotonin (5-HT) system including 5-HT receptors may be involved in mood disorders. We studied 5-HT2A receptor exons and the adjacent intron regions in 102 patients with mood disorders (71 depressive disorders and 31 bipolar disorders). In 34 mood disorder cases, the gene encoding the 5-HT1A receptor had been sequenced, but no disease-specific polymorphism was found. The substitution of C for T at position 102 in exon 1, which had been reported by Warren et al., was confirmed. The corresponding amino acid, serine, did not change. The allele frequency of C [corrected] at position 102 was significantly higher in patients with depressive disorders than in those with bipolar disorders and healthy control subjects. Furthermore, the mean age of onset in the patients heterozyous for the T and C alleles was lower than that in those homozygous for the C allele. No other polymorphism in the gene was found.

Adolescent↗
PubMed1997

Genetic predictors of common disease: apolipoprotein E genotype as a paradigm.

PURPOSE: Genetic variation of a common genetic polymorphism at the structural locus for apolipoprotein E (apoE) has been associated with risk of elevated serum lipids, coronary artery disease, and Alzheimer disease, all of which are multifactoral disorders and are inherited in a complex fashion. Although the apoE polymorphism is only one risk factor in a complex pattern of inheritance, it gives us a foothold into the understanding of the genetic architecture of these disorders. However, apoE also exemplifies the complications that can arise in the use of genetic markers to predict disease. This paper considers the study of apolipoprotein E genotype effects as an example of the following analytical complications: changes in allele frequencies and allele effects with age, pleiotrophic effects of genetic loci, the existence of more than one alternative allele at a locus, and the expectation of a variety of interactions. METHODS: Publications that exemplify these complications are cited and discussed. No original analyses are presented. RESULTS: There is evidence that the relative frequency of the apoE epsilon4 allele declines with age after the sixth decade of life and that the effects of the APOE allele on lipids also may be age-dependent. Grouping of genotypes may not accurately characterize the effects of individual genotypes. Interactions between APOE genotype and a number of factors, including family history of dementia, are demonstrated for the effects of APOE in Alzheimer disease as well as for the effects of apoE on serum lipids. CONCLUSION: Careful attention must be paid to these and other analytical issues when genotype is a predictor.

Alleles↗
PubMed2001

A pseudo-likelihood method for estimating effective population size from temporally spaced samples.

A pseudo maximum likelihood method is proposed to estimate effective population size (Ne) using temporal changes in allele frequencies at multi-allelic loci. The computation is simplified dramatically by (1) approximating the multi-dimensional joint probabilities of all the data by the product of marginal probabilities (hence the name pseudo-likelihood), (2) exploiting the special properties of transition matrix and (3) using a hidden Markov chain algorithm. Simulations show that the pseudo-likelihood method has a similar performance but needs much less computing time and storage compared with the full likelihood method in the case of 3 alleles per locus. Due to computational developments, I was able to assess the performance of the pseudo-likelihood method against the F-statistic method over a wide range of parameters by extensive simulations. It is shown that the pseudo-likelihood method gives more accurate and precise estimates of Ne than the F-statistic method, and the performance difference is mainly due to the presence of rare alleles in the samples. The pseudo-likelihood method is also flexible and can use three or more temporal samples simultaneously to estimate satisfactorily the NeS of each period, or the growth parameters of the population. The accuracy and precision of both methods depend on the ratio of the product of sample size and the number of generations involved to Ne, and the number of independent alleles used. In an application of the pseudo-likelihood method to a large data set of an olive fly population, more precise estimates of Ne are obtained than those from the F-statistic method.

Algorithms↗
PubMed1998

Biochemical differences between products of the ADH locus in olive fruit fly (Bactrocera oleae).

Purified alcohol dehydrogenases from olive fruit flies of genotypes SS, II, and SI were biochemically compared. The enzymes were found to differ in the specific activity, in the influence of pH and temperature on activity, and in the affinity with different substrate-alcohols. The probable relationships of these findings with the dramatic changes in allele frequencies observed when natural populations are introduced in the laboratory are discussed.

Alcohol Dehydrogenase↗